BCH 201: Introduction to Biochemistry 2024-2025 PDF

BCH 201: INTRODUCTION TO BIOCHEMISTRY Dr O.J. Avwioroko’s Part: Introductory chemistry and classification of proteins. Primary, secondary, tertiary and quaternary structures of proteins. Biological functions of proteins. Methods of their isolation, purification and identification. Basic...

BCH 201: INTRODUCTION TO BIOCHEMISTRY Dr O.J. Avwioroko’s Part: Introductory chemistry and classification of proteins. Primary, secondary, tertiary and quaternary structures of proteins. Biological functions of proteins. Methods of their isolation, purification and identification. Basic principles of tests for proteins and amino acids. What are Proteins? Mention some sources of Proteins from the images. What are Proteins?  Proteins are macromolecules made up of monomers called amino acids. Hence, the building blocks of all proteins are called Amino acids.  An amino acid is a simple organic compound consisting of a basic group (-NH2), an acidic group (-COOH), and an organic R group that is unique to each amino acid.  Proteins can also be defined as highly complex macromolecules consisting of one or more long chains of amino acids linked together by peptide bonds.  A protein is a macronutrient that is present in all living beings and is directly involved in various metabolic pathways.  Proteins are species-specific and are unique to each organism. Similarly, these are also organ-specific in that the proteins of the brain are different from those in the muscles.  Proteins are made up of 20 different amino acids, and the property of a protein molecule is a function of the amino acids present.  Plants are capable of synthesizing all amino acids necessary to make proteins, whereas animals cannot.  Amino acids in proteins are linked together by peptide bonds that are formed between the NH2 group of one amino acid to the COOH group of another amino acid.  Proteins are also termed polypeptides, as they are long chains of amino acids connected by peptide bonds. Synthesis of peptides or peptide bonds  A peptide is a short chain made up of amino acids.  Peptide chains are formed when two or more amino acids are connected to each other by peptide bonds.  For every one peptide bond formed between two amino acid residues, there is a loss of one molecules of water (H 2O).  A peptide chain can have as few as two amino acids.  Peptides are categorized into different groups based on the number of amino acids present in the peptide; peptides with two amino acids are termed dipeptides; those with three amino acid residues are called tripeptides (e.g glutathione which is made up of cysteine, glutamic acid and glycine). However, peptides with more than ten amino acids are termed polypeptides.  The peptide bond formed in proteins is a special type of amide bond that exists between two molecules of amino acids, where an α-carboxyl group of one molecule combines with the α-amino group of another molecule. What are polypeptides?  Polypeptides are long chains of amino acids where more than ten amino acids are linked together by peptide bonds.  One or more polypeptides linked together form a protein.  One end of a polypeptide has a free amino group called the amino- terminal or N-terminal, whereas the other end has a free carboxyl group called the carboxyl-terminal or C-terminal.  The sequence of amino acids in a polypeptide is determined by the codons present in the messenger RNA from which the polypeptide is translated.  The sequence of codons in mRNA, in turn, is dependent on the nucleotide sequences in the DNA molecule. Properties of Proteins 1) Solubility in Water Proteins are generally soluble in water or dilute salt solutions. 2) Denaturation and Renaturation Proteins can be denatured by agents such as heat and urea that cause the unfolding of polypeptide chains without causing hydrolysis of peptide bonds. The denaturing agents destroy secondary and tertiary structures, without affecting the primary structure. If a denatured protein returns to its native state after the denaturing agent is removed, the process is called renaturation. Some of the denaturing agents include Physical agents: Heat, radiation, pH Chemical agents: Urea solution which forms new hydrogen bonds in the protein, organic solvents, detergents. 3) Buffering capacity Proteins have buffering capacity; this refers to their ability to resist slight changes in pH thereby behaving as buffers. The buffering capacity of proteins is due to the presence of carboxylic groups and 4) Coagulation When proteins are denatured by heat, they form insoluble aggregates known as coagulum. All the proteins are not heat coagulable, only a few like the albumins and globulins are heat coagulable. 5) Isoelectric point All proteins have isoelectric points. The isoelectric point (pI) is the pH at which the total number of positive charges in a biomolecule equals the number of negative charges, and the overall charge (net charge) becomes zero. At this point or pH, when subjected to an electric field the proteins do not move either towards the anode (positive electrode) or cathode (negative electrode); they become stationary. This property is used in isolation of proteins of interest from a pool. 6) Molecular Weights of Proteins The average molecular weight of an amino acid is taken to be 110 g/mol or Daltons. The total number of amino acids in a protein multiplied by 110 gives the approximate molecular weight of that protein. Different proteins have different amino acid compositions and hence their molecular weights differ. 7) Maximum absorption wavelength  Proteins absorb ultraviolet (UV) light at a maximum wavelength of 280 nanometers (280 nm) unlike nucleic acids (DNA) which absorb UV light at a maximum wavelength of 260 nm. 8) Posttranslational modifications  This occurs after the protein has been synthesized on the ribosome.  Phosphorylation, glycosylation, ADP ribosylation, methylation, hydroxylation, and acetylation affect the charge and the interactions between amino acid residues, altering the three-dimensional configuration and, thus, the function of the protein. Protein Bonding  Besides the primary peptide bonds, several other secondary bonds are responsible for the formation of the stable net structure of proteins. Some of the common secondary bonds present within proteins are: 1. Hydrogen Bonds A hydrogen bond is formed in proteins because of the tendency of a hydrogen atom covalently bonded to an electronegative atom to share electrons with the adjacent atoms like O or N. In a peptide bond, hydrogen bond can be observed as below: -C=O∙∙∙∙∙∙∙∙∙∙∙∙HN- The dotted line between oxygen and hydrogen atoms in peptide linkage represents a hydrogen bond. Hydrogen bond in protein is important as it stabilizes the secondary structure of proteins. 2. Ionic Bonds Ionic bonds in proteins are observed between the acidic and basic groups of the constituent amino acids. Electrostatic interactions also exist between differently charged groups present on the side chains of amino acids. Ionized groups are involved in stabilizing interactions between protein and other molecules rather than stabilizing the protein structure. These ionic bonds, although weaker than the hydrogen bonds, are Ionic bond between Glutamic acid and Lysine 3. Disulfide Bonds The disulfide bond is the second type of covalent bond found between amino acid residues in proteins and polypeptides. This bond is formed by the oxidation of the thiol or sulfhydryl (-SH) groups of two cysteine residues to yield cysteine. Even if the disulfide bridges are very strong when compared to the strength of noncovalent bonds, they are of short-range and can only stabilize the tertiary structure once the bond is completely formed.  Cystine Disulfide Bonds formed between thiol groups of Cysteine residues 4) Hydrophobic and Hydrophilic interactions Hydrophobic interactions occur between the side chains or essentially hydrophobic R groups. Hydrophobic groups unite among themselves, causing the elimination of water to form linkages between various segments of a chain or between different chains. Hydrophobic interactions might also lead to other bonds like hydrogen bonds or ionic bonds between other groups. The hydrophobic bonds also aid other protein interactions, for example, the formation of enzyme-substrate complexes and antibody-antigen interactions. Hydrophilic interactions result in hydrogen bonding between electronegative atoms and hydrogen atoms.